Paper Citation with more information: Nissenson, Michael & Si, Dong. (2017). Automated Protein Chain Isolation from 3D Cryo-EM Data and Volume Comparison Tool. 685-690. 10.1145/3107411.3107500.
Important Note: If your trying to isolate the volume around a mmCIF file, please use the following online converter tool to convert it to a PDF file- http://mmcif.pdbj.org/converter/index.php?l=en There are known bugs that may occur if another tool (such as Chimera or Open Babel) is used to convert between the file types.
Currently contains the source code for Volume Cut and Volume Compare and all includes that are required to run it.
Compiled Source Code can be found in /LinuxCompiled folder.
UCSF Chimera extension module can be found in the VolumeCut_ChimeraExtension_Windows folder. Below are step-by-step installation instructions:
Create a new folder, then place the VolumeCut_ChimeraExtension_Windows folder from the repository into it.
Open UCSF Chimera and select Favorites -> Add to Favorites/Toolbar
Click the add button in the tools menu.
In the "Add Extension Directory" menu, navigate to the folder one level above the VolumeCut_ChimeraExtension_Windows folder. Do not select the VolumeCut_ChimeraExtension_Windows folder itself, rather you must select the folder in the file structure one level above.
After selecting the folder one level above the VolumeCut_ChimeraExtension_Windows folder, select save.
Back on the UCSF Chimera menu, navigate to Tools, select Utilities, then select VolumeCut.
The volume cut window should now appear. They will be blank until a MRC and PDB are loaded.
Load a MRC file and fitted PDB file in UCSF Chimera. For this example, I used EMDB-2513 and PDB-4ci0.
Fill out the Resolution of the MRC file (3.36 is the stated resolution) and desired Radius to cut. A radius of 2.5 was selected as it selects most of the information from a chain without cutting too much voxel data.
Once all information has been filled out and selected, click the Cut Volume button. This then isolates the PDB chain selected, the voxels surrounding the chain, and then loads the results in UCSF Chimera. Below the original volume voxel data has been made transparent to highlight the cut volume data (in yellow).
To save the cut MRC, select the cut volume in the volume viewer, then go to File -> Save map as...
To save the cut PDB, navigate to the main UCSF Chimera tool-bar menu, navigate to File -> Save PDB...
